More posts like this
-
HTseq doesn't support Multi-Threading ?
written by rlatjsgns129 •Hello, everyone ! I'm looking for a way to use HTseq with multi-thread. I couldn't find any options about multi-thread. Anybody knows how to, please …
-
Forum: Feedback on Read Alignment Programs
written by madischapel •Hey everyone! I'm a microbiology undergrad in the middle of completing a work term with a bioinformatics team. My project for the semester involves researching …
-
NCBI genome version vs published genome version - what's 'better'?
written by BiogeekFor organism of choice: A sea anemone (Exaiptasia), there are two versions of the genome available. The original published genome and the NCBI based genome. …
-
How can i use combination of both -nct and -nt in GATK?
written by mandecent.gupta •Is there any way to use `-nct` and `-nt` both to speed up the computation in GATK pipeline?
-
how to set reporting options for RNA-seq reads alignment with hisat2?
written by epigeneHi I'm new to analyzing RNA-seq data. I started with using hisat2 to align RNA-seq reads. I think my main goal is to do differential …
-
Is there any fixed limit on the number of threads in running Tophat?
written by tunl(1) I know that the number of threads specified (-p option) should not be larger than the number of cores available in the system. But …
-
Tophat And Multiple-Mapped Reads
written by Biomonika (Noolean)<p>I would like to ask about update on this topic:</p> <p><a href='http://seqanswers.com/forums/showthread.php?t=24270'>http://seqanswers.com/forums/showthread.php?t=24270</a></p> <pre><code>-g/--max-multihits <int> Instructs TopHat to allow up to this many alignments to the …
-
Why Is Tophat Reporting Secondary Alignments Even When The Option To Do So Is Turned Off
written by Varun Gupta<p>Hi Everyone</p> <p>I am working with Rna seq data and for that i am using TOPHAT aligner.</p> <p>I came across 2 options in tophat which …
-
Thread Safe C/C++ Libraries For Sequence Alignment
written by Tianyang Li •<p>Hi,</p> <p>Are there thread safe C/C++ library for sequence alignment?</p> <p>I was checking out <a href='http://www.seqan.de/'>Seqan</a>, but in the documentation it wasn't explicitly stated that …
-
Parsing Jackhmmer Output
written by Pawel Szczesny<p>What are the options available to parse output (full output with alignments) from jackhmmer? As far as I can test, BioPerl hmmer module isn't able …
Don't think so. You can check all available lastz options by running
lastz --help.